The Daily Transcript

Daily news and views from a postdoctoral fellow in Cell Biology.UCACACCUGGUGGAAGCUCUCUACCUAGUGUGCGGGGAACGAGGCUUCUUCUACACACCCAAGACCCGCCGGGAGGCAGAGGACCUGCAGGUGGGGCAGGUGGAGCUGGGCGGGGGCCCUGGUGCAGGCAGCCUGCAGCC

Tuesday, November 29, 2005

Facts and Models

"Some scientific studies are based on pure facts..while others stand on theory alone."

Actually that's not true. Science generates models (i.e. theories) that predict how the world works. To verify that your model is the "best available model", you must perform experiments (or make observations) to test the model's predictive power. The results of these experiments (i.e. facts, or empirical results) either support your model or go against your model. The latter scenario is called falsification. If your model is falsified, you either have to alter your model or throw it away and come up with a better model. This is the scientific method.

Do not confuse empirical results with models (or "theories"). They play very different parts within the scientific process. The rock that falls towards the earth with a certain acceleration is an empirical result, and gravity is the model. Gravity would predict that a rock falling towards the moon has a different velocity, and so it does ... thus our current model of gravity is supported by the facts (i.e. the theory of gravity is not yet falsified).

Some models can't be falsified. These models are "bad" because they do not have predictive power. For example if I believe the model that God created the universe, it does not predict anything WITH CERTITUDE. It does not predict "If you dig here you will find X" ... in other words, there is never a chance that you would dig and find "not X" and thus proclaim, "ah, I guess this falsifies God". This is not to say that God does not exist, but that the question of whether God created the universe lies beyond the realm of Science.

In other words good models exclude many potential results. A fantastic model would predict A and not B, C, D, E, F, G or H. A weak model would predict either A, B, C or D, and not E, F, G or H. Non-falsifiable models would not give any clear prediction (A to H are possible). Many people believe that string theory is not a good model because it's details can be molded to fit any empirical result and thus string theory (in it's current form) has almost no predictive power. Evolution on the other hand has very strong predictive power and those predictions are seen within every sequenced gene.

To sum this up,

1) Science builds models (i.e. theories).2) Models (i.e. theories) have a certain degree of predictive power with regards to the empirical results (i.e. facts) you accumulate through experimentation and observations. The better the model the more accurate the predictions.3) Fantastic Models usually give insight. This means that you acquire a deeper understanding of the underlying principals at play. Some may argue that good models encourage reductionalism.

Sunday, November 27, 2005

Thelonius Monk & Asperger's Syndrome

For oncetoday's entry will be on a muscician, Thelonius Monk.

This great artist has been in the news lately - recently someone acting on rumors found a recording of a Carnegie Hall concert given by the Thelonious Monk Quartet and John Coltrane. This new recording is of great importance as John Coltrane spent 6 pivotal months with Thelonious in 1957. In that time he kicked heroin and "found God". Until this discovery there were only a hand full of songs recorded by this partnership. I've been listening to this phenomenal recording for 2 weeks straight, it's fantastic.

Monk's music is incredible. Paraphrasing Wynton Marsalis, he has the spirit of a wise guru trapped inside the mind of a five year old. When I've made my parents listen to his stuff, they exclaimed that his songs sounded like Sesame Street on LSD.

His unorthodox music, fully of seemingly simple yet complex and melodies, and his personality (Monk seems oblivious to the world - totaly foccused on his music) are all reminiscent of Asperger's syndrome. This disease has been in the news of late. Asperger's is a form of Autism, but the afflicted are usually quite gifted especially when it comes to recognizing and analyzing patterns. I've writen in the past on how Asperger's and other forms of Autism may be caused by increased prenatal exposure to testosterone. In a recent article, WIRED claimed that it was the Nerd Syndrome:

Kathryn Stewart, director of the Orion Academy, a high school for high-functioning kids in Moraga, California, calls Asperger's syndrome "the engineers' disorder." Bill Gates is regularly diagnosed in the press: His single-minded focus on technical minutiae, rocking motions, and flat tone of voice are all suggestive of an adult with some trace of the disorder. Dov's father told me that his friends in the Valley say many of their coworkers "could be diagnosed with ODD - they're odd." In Microserfs, novelist Douglas Coupland observes, "I think all tech people are slightly autistic."

...

These days, the autistic fascinations with technology, ordered systems, visual modes of thinking, and subversive creativity have plenty of outlets. There's even a cheeky Asperger's term for the rest of us - NTs, "neurotypicals." Many children on the spectrum become obsessed with VCRs, Pokemon, and computer games, working the joysticks until blisters appear on their fingers. (In the diagnostic lexicon, this kind of relentless behavior is called "perseveration.") Even when playing alongside someone their own age, however, autistic kids tend to play separately. Echoing Asperger, the director of the clinic in San Jose where I met Nick, Michelle Garcia Winner, suggests that "Pokemon must have been invented by a team of Japanese engineers with Asperger." Attwood writes that computers "are an ideal interest for a person with Asperger's syndrome ... they are logical, consistent, and not prone to moods."

And other great muscicians, such as Glenn Gould, have been diagnossed with this syndrome. To hear about Asperger's on NPR's Infinite Mind click here.

Saturday, November 26, 2005

Quote from Ernst Mayr

It is often asked why we do science? Or, what is science good for? ... The insatiable curiosity of human beings, and the desire for a better understanding of the world they live in, is the primary reason for an interest in science by most scientists. It is based on the conviction that none of the philosophical or purely ideological theories of the world can compete in the long run with the understanding of the world produced by science.

Friday, November 25, 2005

Thanksgiving dinner talk & outsourcing

Last night we had many coworkers over for a thanksgiving food orgy. Everything was great, although it took forever to cook our 27lb turkey. We had many things to celebrate. One coworker just got a paper accepted into a big journal. Another coworker is leaving us to start his own lab on the west coast. At dinner the talk drifted from work to my blog, then to outsourcing science, then to how some scientists who used to be communists act like capitalists, and finally how there is one lab head at Harvard Medical School who's already outsourcing all of his fly work (i.e. creating and maintaining mutant fly strains). Apparently the NIH does not fund any outsourced science work (yet).

Since today's post was already written for me, our guests then suggested a couple of entry titles, the only one that I can recall is "Some scientists are more equal than others".

Wednesday, November 23, 2005

Marc Kirschner to give a reading of his new book

This morning someone took our paper, and so during breakfast I picked up The Improper Bostonian to check the local listings ... and who do I see listed in the Books & Poetry section? Our ex-department head Marc Kirschner. To be honest, someone had told me that he was in there - but they had a photo of him (and of his long time collaborator, John Gerhart) as well.

He'll be reading from his new book The Plausibility of Life, November 29th, 7PM at First Parish Church, Harvard Square. To read a previous entry on this book, click here.

Tuesday, November 22, 2005

Back from NYC

Well I'm back from NYC where I once was a Grad student in the Gundersen Lab. My wife and I try to go back to "the city" once every 3-4 months to "get stimulated" (click here for a description of a previous visit).

So what did we do?

We spent Saturday night at "Chez Bushwick", watching their Shtudio Show ... from the website:

SHTUDIO SHOW offers a smorgasbord of cutting-edge dance, new music and other performance. This is not another burlesque/cabaret show, but rather an evening devoted to maintaining New York's unique legacy of experimentation and underground umph.

Although SHTUDIO SHOW seemed to be frequented by mostly modern dancers, the show included readings, performance art, music (although of the postmodern genre) and of course a dance performance (again very postmodern).

So where is "Chez Bushwick"? Well in Bushwick Brooklyn, NY of course ... from the April 1st edition of the NYTimes:

Williamsburg and neighboring Bushwick buzz with ad hoc entrepreneurship. Artists brave the area's stark postindustrial landscape, and camp out -- often illegally -- in loft spaces. Soon enough, fabulous little health food stores spring up among the carcasses of burned-out cars, rents rise accordingly, and artists push on to the next frontier, leaving in their wake a neighborhood made safe for commerce but too expensive for artists. It has happened before -- think SoHo and the East Village -- and it may well be happening again. Artists in search of affordable space have been pushing Williamsburg's eastern frontier steadily deeper into Bushwick.

Although Williamsburg is gentrifying, Bushwick is all abandoned industrial space. And Bushwick is being invaded by artists, from the same article:

The most visible addition (to the dance scene)was the Williamsburg Art Nexus, a black box theater affectionately known as WAX. A refuge for up-and-coming choreographers that opened in 2000, it reflected the neighborhood's freewheeling, do-it-yourself roots. Unlike Manhattan spaces, where a handful of gatekeepers control access to sought-after sites like P.S. 122, Dance Theater Workshop, Danspace Project at St. Mark's Church and the Kitchen, WAX was uncurated. Anyone with $1,500 and a dream could rent the theater for a weekend and put on a show, until last fall, when the theater closed to make way for luxury lofts.

No site dedicated to dance has emerged in the area with the visibility and professionalism WAX had, but Williamsburg and Bushwick are still full of dance studios that serve intermittently as theaters. Chez Bushwick, Soundance and Studio 111 all have informal monthly performance series, and there has been a flowering of mixed-use spaces, like Galapagos Art Space, the Brick and OfficeOps, offering the occasional dance performance. In addition, some choreographers use their private lofts for showings, and a few art galleries, like the Williamsburg Art and Historical Center and Cave, have regular dance performances.

This flourishing has given the dance world a much-needed boost. Cheap space and ample time have helped young choreographers push past the generic stuff they were churning out in two-hour increments at rented studios, and the multiplicity of informal performance spaces has encouraged irreverence and experimentation.

A documentary on the place is in the works. For more on Chez Bushwick here.

Another visit of note, PS1, MoMa's experimental contemporary art museum located in an industrial section of Queens (right across thr river from Bushwick). With a NYC trip, we almost always make a quick stop at PS1. The most notible installation was John Kesler's The Palace at 4 A.M.What was it about? It's a room full of moving cameras ... filming you through paper cutouts that depict war, pornography and 9/11. Thus the viewer is viewed and all is distorted (see pic). In one instalation, post cards are slowly ramed into cameras, and on the video screen you're flying into the World Trade Center. Another camera is pointed towards a window where a carboard cutout is hanging ... and on the screen it's the Apocalypse on Jackson Ave. Is terrorism and the war, an ugly pornographic flick? How would we feal if we were there? How is the media distorting all these events?

Friday, November 18, 2005

What a week

Well this week was a mixed bag.

My microinjection experiments were painful due to the fact that the needles kept braking and that Hela cells are just hard cells to microinject (see a pic of injection bellow). These days of pain may explain the outbursts on previous posts.

Thursday, November 17, 2005

The Economics of Academic Research

Interesting exchange will the Tall Medstudent. That I’d like to share as a post on it’s own. (All that follows is an elaboration of comments from yesterday-post’s).

Tall Medstudent:

When foreigner postdocs stop coming to the US, there will have to be a rise in salaries, and that will be followed by Americans reentering science.

That will be helped by the worsening of the US economy; the worse opportunities are in business, the better jobs in science will look.

This comes back to the Bush State-of-the-Union statement: America needs foreigners to do the jobs that Americans will not do. The lie in that statement was that Americans will not do the jobs, because American business would rather pay foreigners a lower wage than pay an American what he needs to survive in his economy. Anyways, I think that the US science needs a shake-up like this in order to move forward again.

I agree partly. Salaries will go up if there is a decrease in labor supply. All those that claim that “Americans don’t want to do those jobs” DON’T UNDERSTAND ECONOMICS. A truer statement is that Americans don’t want to do those jobs AT THAT PRICE. When employers can’t hire, they increase the salaries until they can fill those positions.

BUT an additional factor, that has non-monetary value, is how respected a job is. Americans don’t respect academia and so not many Americans enter research. In contrast Asian culture respects academia – that’s why many Americans of Asian descent enter academia at higher rates than other subsets of the American population. This not only has effects on how many Americans enter Science, but how much federal (or state) money is set aside for basic research, and what the NIH guidelines are to paying postdocs. The stature of a postdoc is so low in our society (and in our institutions) that they’re position on the income ladder is lower than it reasonably should be. And the high number of postdocs (due mostly to the over hiring of postdocs) applying for the limited number of PI slots is another great source of anxiety and one of the biggest problems in academia.

The solution may not be to limit foreign students, especially if other countries get their act together and the American school system continues to fail in its mission to produce well educated citizens. To build a wall around the US would only isolate America from obtaining the best minds from overseas. This is exacerbated by the fact that foreign researchers are treated like crap when they are here (in terms of getting visas and green-cards). I’ll get back to what the solution IS later, now onto part two …

I disagree with the worsening US economy will increase academic pay.

1) When this occurred earlier this decade, Americans jumped from business to the high paying professions (doctor, lawyer ...). There are too many alternatives to academia.

2) If the economy slides downhill, the government will cut money for research grants. Less postdoc openings and thus the market will favor lowering salaries even more (fewer jobs for the pool of aspiring academics).

3) Even if academia seems like a better alternative, the increase in Americans in academia will favor an even greater lowering in salaries and work conditions (as in #2 the ratio of jobs to the employment pool decreases, pushing salaries down).

Academic research is in a sense a luxury. A country has it if it can afford it. But that is deceptive. The US economy relies on basic research to generate new industry, so more and more it is a necessity. That’s why China and Singapore are investing tons of money in biomedical science. That’s why the US economy has been so strong over the last 60 years – it has the best universities and generates all the new technology. But I’m not sure that this will last. My belief is that academic investment is primarily correlated to HOW MUCH THE GOVERNMENT WANTS TO INVEST IN RESEARCH. Right now support for research funding is eroding. Academic conditions (FOR POSTDOCS AND GRADSTUDENTS) are not good, but still better than overseas. And the reliance on foreign academics allows this to continue to a certain extent. But I believe that the main problems are within American culture and academic culture.

Recently the NIH guidelines for postdoc salaries went up. Why? It wasn't because of supply and demand issues, it was because members of academia (PIs, not postdocs) lobbied the NIH to increase the salaries.

So in the end factors within the Academic establishment, and factors within American culture (as in respect for researchers, and a recognition that research is important for the future of this country) are the biggest pressures that will better conditions in Academic institutions especially for postdocs. We (POSTDOCS) need more money, and better respect within the institution and within society. And less postdocs should be hired, but those that are hired should be nutured not treated like slave labor! We can’t just rely on the market, but must change the culture as well. American culture and Academic culture. To simply rely on the market would be a disaster for postdocs, for the US, and in the end the US will lose out.

America, Foreigners, and Academic Science

Foreign graduate students, particularly those who study science or engineering,are a boon to the American economy and education system. They are critical to the United States' technological leadership in the world economy: according to a study by Keith Maskus, an economist at the University of Colorado, for every 100 international students who receive science or engineering Ph.D.'s from Americanuniversities, the nation gains 62 future patent applications. International students have founded many of America's most innovative companies, including Sun Microsystems and Intel.

America needs academics. We support the US economy. But grad-students and postdocs in academic labs are treated like crap here - low wages, little security. Keep in mind however that conditions in the US are much better off than elsewhere, and most of the big labs where you can get the best trainning are still American labs. Result - very few Americans are in research and thus the US relies on foreigners to fill it's academic institutions. But can this go on? The number of academics coming across the border to work in the US is falling.

Although it's easy to blame tightened post-9/11 visa policies for stagnating or declining international student enrollment figures, other factors have contributed to this unfortunate trend. Among them are fierce competition for students with Britain, Japan and other countries; improvements in the economies and universities of China and India, the countries that send the largest number of students here; the cost of an American education; and a perception that the United States is not interested in attracting international students.

And furthermore, what's happening to foreign academics after they're finished with their gradstudies and postdocs at American institutions? Many, unable to get permanent status, are leaving. I personally know 4 individuals in my direct working environment who are dealing with green cards and are in limbo with regard to their current residency status.

Finally, and perhaps most avoidably, the United States makes it exceedingly difficult for our foreign-born science and engineering doctorates to stay in the country, where they might work in our private sector, conduct research in our labs or teach at our universities. It can take two years or more to gain permanent residency, and there are significant backlogs in applications for employment-based green cards.

Again the US should pay attention to all this if they wish to stay ahead of the curve.

Tuesday, November 15, 2005

Deforestation

Good article in today's Science Section of the NY Times on recent deforestation trends (see map below). Overall deforestation is not as rapid as in the past. And a surprise! Can it be that "totalitarian China" is outplanting the other developing nations?

From the article:

"While good progress is being made in many places, unfortunately forest resources are still being lost or degraded at an alarmingly high rate," said Hosny El-Lakany, assistant director-general of forestry for the food and agriculture agency.

The slowing rate of forest loss is encouraging, some forest experts say, but biologists contend that most acreage gained by plantation forestry contains a fraction of the plant and animal diversity destroyed with virgin forests. Forest cover has generally been expanding in North America, Europe and China and diminishing in the tropics.

...

Asia has seen an extraordinary turnaround in a decade: it lost about 3,000square miles of forest a year in the 90's but gained nearly 4,000 annually since2000, said Mette Loyche Wilkie of the F.A.O. But almost all of that change hasoccurred because of China's new forest policy, she said. Tropical forestselsewhere in Asia are still being cleared at a rising pace, the report said.

While Africans and South Americans cut down their trees, the Chinese are planting them (as well as the Spanish and Italians). And this is less of a credit to China and more of wake up call to countries like Brazil and Indonesia. If you're going to cut trees, plant them as well! It's called renewing your renewable resources. For more info see the Food and Agricultural Organization of the UN.

But why Clemson and Trudeau? Both have small life-science departments, both are in the middle of no-where. More importantly, both do not not have many scientists pushing the frontiers of knowledge. There are many essentials to create a good working environment, but stimulation is near the top. Sure these places may have low stress levels and great health care benefits, but stimulation? It reminds me of these stupid lists of the "best places to live in America" where Nirvana lies in some tiny town in the Midwest. Something tells me that these lists reflect the wishes of the list makers rather than some objective measurement.

There are many things I hate about Harvard Medical School, but one benefit is that you are surrounded by hard working and/or very clever people. In most labs, such an environment helps you grow as a scientist. And Boston also has quite a bit of culture and night life to help recharge your batteries.

Is Harvard Medical School in the top 15? No. Would I rank it in the top 15? Probably not.

Harvard medical school is a great place to work as a postdoc, but not as junior faculty. Unfortunately Harvard can rest on i's name and can treat it's academic staff like trash ... and get away with it. After all there will always be more high quality academics vying for those spots. But would I want to go to Clemson or Trudeau? Not anytime soon.

Thursday, November 10, 2005

Transcriptional Activation

Yes the daily transcript has an entry on TRANSCRIPTION.

Yesterday I attended a talk given by Robert Tjian from UC Berkeley (HHMI profile). So what is new in the world of transcription?

Well he gave a nice intro. He explained how his lab first thought about the problem, then conducted "promoter bashing" experiments to identify DNA regions important for activating flanking gene sequences. Then he presented the current model. Promoter and enhancer DNA regions that flank the gene, bind proteins (i.e. transcription factors or TFs) that interact with a big complex ... TFIID. This complex includes the TATA binding protein (TBP) and Tata binding factors (TAFs). Under the influence of TFs, TFIID unzips the DNA and recruits RNA Polymerase II, the enzyme that copies the gene's DNA sequence into mRNA (this copying process is called "TRANSCRIPTION").

So the big question is how is transcription spatially and temporally regulated? In other words how do different cells turn on different genes? And how does the same cell turn on different genes at different times (such as during development)?

The answer? As far as I can tell confusion. We know that different TFs and different TAFs are expressed in different cells, we know that the whole thing is complex ... but beyond these simple statements, Prof Tjian could not offer further insight. I left the talk with "a bad taste in my mouth" (sorry for the cliche).

Something needs to happen in this field for it to make some serious progress. Perhaps the idea of picking model genes or understanding how one gene is differentially activated in different cells at different times, is not the best approach. Another plan of attack is needed.

Perhaps there is some hope - a student who rotated in the lab this summer, joined another lab who's goal is to coat microarrays with small DNA fragments and probe these arrays with labeled transcription factors. In otherwords BIG BIOLOGY. Now I'm no fan of big biology, but maybe it can be used to understand how these various components work together to generate temporal and spatial differential expression of genes.

Tuesday, November 08, 2005

Incredible International Kits

All this talk of kits, and outsourcing science ... then my boss (Tom) comes back from Japan where at a conference he met a guy who operates a biomedical company that sells purified components for in vitro translation (remember from the Central Dogma, translation = "mRNA => protein"). Anyway using this company's reagents, one can reconstitute translation with purified components, and the company will sell you each purified component separately!

Want to have ribosomes bound to mRNA and stalled after encountering a valine codon? Reconstitute the whole reaction without the valine tRNA! (Actually such experiments have been done.) Want to stall the ribosome at the stop codon, omit release factors. It's all yours if you have the $.

One catch - these reagents are not for sale overseas ... so here is another wrinkle in the whole science outsourcing issue, the transport of biological reagents over borders. Currently there are many restrictions (just ask anyone who sent/received antibodies from labs overseas) and it is not clear how these restrictions will change over time. With terrorism and the promotion of globalization, it's hard to predict the future of international biomedical business.

Monday, November 07, 2005

France is on Fire

Well if you're not American, you probably know all about the chaos that is going on in France. You know about the two kids electrocuted by accident while hidding from police officers, who relentlessly target the minority youths in empoverished French suburbs. You know about the riots, the words of the Interior Minister Nicolas Sarkozy, the and now 10 officers injured in the latest clash. From the BBC:

FRENCH RIOTSOne man killed4,700 cars torched1,200 people arrested17 people sentenced108 police and firefighters injuredFigures as of 7 November

Of course some idioblogs think that this is "terrorism", "Islam" or "Islamofascist". If you want to know what is the cause - just look at the Watts County riots here in Uncle Sam's backyard.

One question that I have: Why isn't this story being reported in the US?

Saturday, November 05, 2005

Interview With a Tall Medstudent

Last night I conducted an interview with the Tall Med Student (over Microsoft Instant Messenger). Like me, the Tall Med Student is Canadian although for a while he was an ex-pat working as a postdoc in some lab at Harvard Medical School (as I am now). Currently, he is attending Medical school at the University of Calgary, and has his own blog (Tales of a Tall Medstudent). We talked about the whole US/Canada thing, Alberta, medschool, and aliens ...

Mad Scientist says:How does it feel to leave the US and be back in Canada (in ten words or less)?Tall Med Student says:It's a pleasure to go see a doctor up here. I guess that is eleven words, technically.Mad Scientist says:Don't worry, it's like a baker's dozen.Tall Med Student says:Oh good. Now I am thinking about doughnuts.Mad Scientist says:Would you ever reconsider moving back down to the US?Tall Med Student says:Never, not in three years. NYC or nothing, I think.Mad Scientist says:What is the major issue that prevents you from moving back down?Tall Med Student says:Health care. And all my tax money going to bomb-making and murder for profit.Mad Scientist says:Elizabeth Blackburn told me "If I were you I would move to Alberta and get a lab there, they'll have tons of money soon", any comment?Tall Med Student says:Just got 1.3 billion for new health care facilities in Calgary. Every dollar of oil price represents 100 million in income for the provincial government. This year's surplus will be around 9 billion or something.Mad Scientist says:It's often said in Canada (and in Quebec in particular) that Albertans want to be American, any comment?Tall Med Student says:No way.Mad Scientist says:Could you elaborate.Tall Med Student says:Bush has stopped all that.Tall Med Student says:People here are freaking out over the possibility of private health care getting more access to the province.Mad Scientist says:So is there a movement against all these plans to privatize healthcare?Tall Med Student says:The government is looking for a 'third way', by which they emphasize that it will remain a public system, just organized in new ways.Mad Scientist says:As a doctor, are you planning to practice medicine in Alberta?Tall Med Student says:Maybe, docs are stinking rich here. Unbelievably so. A good lifestyle, low stress.Mad Scientist says:Why do they call it "practice"? That terminology freaks me out.Tall Med Student says:'Cause you always need more practice.Mad Scientist says:As a patient I wouldn't want to be practiced on I need the real thing!Tall Med Student says:Hmm, then you need to only be subjected to tried and true techniques, like amputation or bladder surgery. Although, I suppose that current doctors don't have much experience with those anymore.Mad Scientist says:I hear that you've suffered an injury lately - did they have to amputate?Tall Med Student says:No, they practiced on me. A med student sewed me up after the surgery, actually. The plastic surgeon did his residency here, and has just come back to town after doing a fellowship elsewhere.Mad Scientist says:Wow, from U of C?Tall Med Student says:No, U of S. Which worried me a bit.Mad Scientist says:Did you guys chat about med school stuff?Tall Med Student says:Yeah, she was a fourth year, here on an elective.Mad Scientist says:So everyone is flocking to Calgary.Tall Med Student says:Well, I'm not surprised. People go where the oil is.Mad Scientist says:I thought it was the dino bones?Tall Med Student says:The oil is here because of the dino bones, and everyone else is here for the oil, so, I suppose that makes the dino bones the primary reason.Tall Med Student says:Man, I have been trying to figure out who that alien who visited my blog is. I suspect he or she is a Bostonian.Mad Scientist says:Hmm. Aliens visiting blogs - are you on morphine?Tall Med Student says:He or she mentions Salem in his or her blog.Mad Scientist says:Very interesting. OK Dr. J is yanking on my shoulder - it's Happy Hour. Speak to you soon.Tall Med Student says:Okay, gotta run. Ttyl.

Friday, November 04, 2005

NY Times Downgrades Access

It's a shame, but the NY Times has placed limitations on it's website access. Now to view items from the OpEd section, you need to subscribe to the paper. It's obvious why this is bad for readers, but why is it bad for the NY Times? From an interesting post on Technorati's blog:

As the chart above shows, the most influential media sites on the web are still well-funded mainstream media sites, like The New York Times, ...

Infact it's the most linked-to site. And in comparison there is the Wall Street Journal:

An interesting statistic to note is the current placement of subscription sites like WSJ.com (the Wall Street Journal). While the WSJ has begun to offer some content outside of its subscriber-only site, the policy is clearly costing them some influence and attention in the blogosphere, as bloggers find it difficult to link to articles in the subscriber-only sections. Also interesting to note is that even though The New York Times and The Washington Post require free registration to view the articles, bloggers are still linking to the stories, and this behavior hasn't changed much in the past 6 months.

Note that since this change does not affect me (I get the paper at home and have full access to the web edition) I don't write this commentary out of vindictiveness. With the rise of electronic media, institutions like the NYTimes are more accessible and have much influence than previously.

So will the current change in the NY Times' policy affect it's relatively newfound influence? And if we do move to a paperless environment, where the morning news is read through an electronic screen instead of through paper, will more electronic content be pay-per-view? Going electronic and dumping paper is in the end a smart choice for many reasons (i.e. less waste, more cost effective) ... but how will these changes affect the influence of these institutions in the public debate? We will see.

More on the Rise of Chinese Technology

To gain an edge technologically, you need proficiency and creativity. With the rise of the East's Academic Institutions (see my entry on outsourcing science), will the East be able to generate NEW technology? Many have argued "No", but I think that this is mostly Western prejudice. Just look at the innovation coming out of Japan over the past 50 years. From an OpEd by Thomas Friedman in today's NYTimes:

There is a lot of truth to that. Even the Chinese will tell you that they've been good at making the next new thing, and copying the next new thing, but not imagining the next new thing. That may be about to change.

...

Check out Microsoft Research Asia, the research center Bill Gates set up in Beijing to draw on Chinese brainpower. In 1998, Microsoft gave IQ tests to some 2,000 top Chinese engineers and scientists and hired 20. Today it has 200 full-time Chinese researchers. Harry Shum, a Carnegie Mellon-trained computer engineer who runs the lab, has a very clear view of what Chinese innovators can do, given the right environment. The Siggraph convention is the premier global conference for computer graphics and interactive technologies. At Siggraph 2005, 98 papers were published from research institutes all over the world.

Nine of them - almost 10 percent - came from Microsoft's Chinese research center, beating out M.I.T. and Stanford. Dr. Shum said: "In 1999 we had one paper published. In 2000, we had one. In 2001, we had two. In 2002, we had four. In 2003 we had three. In 2004, we had five, and this year we are very lucky to have nine." Do you see a pattern?

In addition, Microsoft Beijing has contributed more than 100 new technologies for current Microsoft products - from the Xbox to Windows. That's a huge leap in seven years, although, outside the hothouses like Microsoft, China still has a way to go.

...

[Dr. Shum] "I learned mostly about how to do research right at Carnegie Mellon. ... Before you create anything new, you need to understand what is already there. Once you have this foundation, being creative can be trainable. China is building that foundation. So very soon, in 10 or 20 years, you will see a flood of top-quality research papers from China."

So it would seem that China is on the rise. (Any news from India now?)

Wednesday, November 02, 2005

Eye Candy

Tuesday, November 01, 2005

A Protein Complex; The Overused Abbreviation

Every subject has it's lingo and it's share of strange terms. Add abbreviations and acronyms, and certain areas of expertise can be almost incomprehensible. Then there is Biology.

Life has a diversification machine, evolution. Thus those who study life (i.e. Biologists) have lots of proteins and genes to name and to investigate. Humans have about 23,000 to 30,000 conventional genes, and many other non-conventional genetic elements such as small RNAs. On top of that these same 23,000+ genes are also found in other vertebrates and many are found in almost every eukaryotic cell. Thus the same molecular machinery in yeast may be completely renamed in humans ... and named weirdly in fruit flies (Drosophila). All this leads to a mass confusion for those that read the biology literature.

But the part that really annoys and frustrates some Biologists is the overused abbreviation - a single abbreviation that is used for several different biological components. The most famous overused abbreviation (as far as I can tell) is APC.

What is APC? Well one thing it doesn't normally stand for is "A Protein Complex".

Ask a cancer biologist, and APC stands for Adenopolyposis Coli, a gene that causes colon polyps. The product of this gene affects several cellular signals and helps organize the cell's cytoskeleton. APC is also mutated in 50-60% of spontaneous colorectal cancers.

Ask a biologist studying the cell cycle what APC stands for, and he will tell you that it stands for the Anaphase Promoting Complex. This molecular machine is responsible for tagetting the destruction of key components so that the cell can proceed along the cell division cycle.

Ask an immunologist what APC stands for, and she may state that it stands for the Antigen Presenting Cell. These cell are exposing foreign antigens to the appropriate white blood cell in order to activate an immunological response.

One abbreviation, three completely different biological items. Enter "APC" into PubMed and ... good luck.

Then one day it was reported that APC (adenopolyposis coli) interacted with the machinery that yanked the chromosomes apart during cell division. This machine is called the kinetochore (greek for moving body). Of course many components of the kinetochores also activate the other APC (the Anaphase Promoting Complex). Activated APC (Anaphase Promoting Complex) destroys the links between duplicated chromosomes so that the act of chromosome separation (i.e. ANAPHASE) can take place. In addition, the first APC (adenopolyposis coli) plays a role in how the cytoskeleton reorganizes during "polarization events". An example of a "polarization event" is when a white blood cell polarizes towards an APC (Antigen Presenting Cells). Some researchers have identified specific versions of APC (adenopolyposis coli) in certain immune cells (perhaps even in APCs!) ... are you confused yet?

The Tower of Babel was built and all those that spoke the same language could no longer communicate.